Avoiding scientific McCarthyism: reversing the recent call to punish Russian scientists

 

A recent call for punishing individual Russian scientists, instead of institutions and political power holders, is a wrong-headed and mean-spirited response to the atrocities of the Russian war on Ukraine.

 

 

 

 

Russia’s illegal war against Ukraine is an abomination of any ethical or moral norm, and Russia deserves to be held accountable and liable for the resulting humanitarian and economic costs. One powerfully employed punishment has been severe and expansive sanctions meant to ply direct pressure on Russia’s economic and political elite.

 

A group of scientists have published an open letter in Nature and are requesting signatories for a call to end scientific cooperation with Russian scientists. This appeal requests that international funders, publishers, societies and individual scientists should immediately endeavour:

 

1.     to block access to all scientometric databases and materials of scientific

publishers for citizens and institutions of the Russian Federation and Belarus;

2.     to make it impossible for researchers affiliated with institutions and scientific

institutions of the Russian Federation and Belarus to participate in international grant programs funded by the European Union and other partners;

3.     to suspend participation of researchers, students and institutions from the

Russian Federation and Belarus in current international academic mobility programs;

4.     to boycott attempts at holding scientific events on the territory of the Russian

Federation and Belarus (in particular, scientific conferences, symposiums, etc.);

5.     to suspend indexing of scientific materials published in the Russian Federation

and Belarus in all scientometric databases;

6.     to prohibit citizens of the Russian Federation and Belarus from being

editors/co-editors/reviewers of international publications.

 

To be clear, these actions will do harm, and are unlikely to effect change in Russian policy. These measures are meant to be punitive. Only number 4 on the list above makes sense.

 

I have Russian scientific collaborators and I have been in contact with them. They use subtle language to communicate their disagreement with Russia's war and that they hope for an end to it. They write e-mails as if someone is watching. Because someone is watching.

 

The political climate in Russia is one that is extremely dangerous for internationally connected Russians and for those who do not agree with or support Putin. Putin recently opined that Russia needed a cleansing and traitors to be spit out like flies. Countless Russians died in previous political cleansings. To demand that scientists renounce the Russian war in order to participate in global funding and information exchange, as the appeal does, is oblivious to the risks individuals face in Russia for expressing views that counter political decrees. This appeal comes across as insensitive and, quite frankly, ignorant.

 

As an Editor of a journal, I strive to ensure that information is disseminated broadly and that we are as inclusive as possible by assembling diverse teams of editors. As the head of a lab, I endeavour to provide opportunities to a diverse group of students and researchers. I have supported and worked with students and researchers from many countries, including some from countries controlled by repressive and authoritarian regimes. I prioritize these types of engagement because I believe that this promotes global inclusion and expands the worldviews of people that can help turn the political tide in their own countries, or to provide leadership when dictators finally fall. 

 

What should we be doing as scientists? We should support Ukraine and Ukrainians, and we should pressure our own governments to do more, including creating a no-fly zone in Ukraine. Further, we should maintain our ties to those inside of Russia and keep the lines of communication open, and let those who are disheartened by what their country is doing that they are still part of the wider world. These international ties might be important for what comes next in Russia.

Dazzling Dolphins in Decline: Conflicts between Conservation and Fisheries

 Guest post by recent UTSC MEnvSc graduate, Samantha Lalonde

How do some people seem to know which career they are going to pursue seemingly before they can even walk? Do they just wake up one morning and decide that they want to be a dentist? In my case, I had no idea what I wanted to do all throughout primary school and most of high school. Then, I was presented with a life-changing opportunity.

 In high school, I was offered the chance to volunteer in the Amazon rainforest in Peru with Operation Wallacea³, a conservation research organization. I lived on a riverboat in the Pacaya Samiria National Reserve⁴ where I completed field surveys of birds, reptiles, fish, and plants with local and international researchers. I quickly realized that I enjoyed doing field work and studying populations of species. But it was one particular morning, while we were gliding peacefully along the narrow river in our small boat, that I realized that I wanted to pursue studies in conservation. A sound broke the silence; the unmistakable sound of a dolphin breaching the surface of the water to breath. It was then that I was introduced to the dazzling pink river dolphin. I had never even heard of these unique charismatic animals until embarking on this trip. But I couldn’t imagine how anyone, after seeing these creatures, could ever harm them.

After pursuing a degree in environmental science and studying the complex ecological, social, and economic factors surrounding conservation science, I now understand that life isn’t as simple as I thought it was in that moment. People have differing beliefs, priorities, and opportunities for education. All of this to say that the Amazonian river dolphins are in decline, and I’m here to explain to past me (and present you since you’re here) why their conservation isn’t such a clear-cut matter.

Boto river dolphin – Mr Devotor / Charismatic Planet¹  

Tucuxi river dolphin – Gregory R. Mann / Ocean Treasures²  

The Amazon basin is home to two dolphin species – the boto or Amazon river dolphin and the tucuxi dolphin. The boto dolphin is larger and completely pink, compared to the tucuxi dolphin, which has a pale pink stomach. The International Union for Conservation of Nature⁵ (IUCN), an organization working on conservation and sustainable use of natural resources, has assessed both dolphin species under the IUCN Red List⁶. The IUCN Red List provides information on global species habitat and ecology as well as threats they are facing. Tucuxi was classified as “Data Deficient” in 2010⁷, meaning that there is limited information on the threats, ecology, and population trends for this species. Up until recently, the boto dolphin was also listed as “Data Deficient”, but in 2018, it was uplisted to “Endangered”⁸ due to studies showing large declines in their numbers.

The uplisting of the boto dolphin to “Endangered” by the IUCN was in part influenced by a study by da Silva and colleagues⁹ in 2018 that looked at long term changes in river dolphin populations. In this study, dolphin surveys were completed monthly from 1994 to 2017 in one of the largest conservation areas of the Brazilian Amazon – the Mamirauá Sustainable Development Reserve (MSDR). Despite being legally protected⁸ (bans on commercial fishing in the reserve), the number of botos counted during the surveys halved every 10 years, and the number of tucuxi every 9 years. Why was this happening? The areas in which the researchers were doing their surveys had not significantly increased in human population, food sources for the dolphins were still abundant, and the region had not been affected by dams or mining. The researchers concluded that there was no other obvious reason for declines in dolphin populations other than fishery-related mortality. They noted that the human population in Amazonia is growing rapidly, and so too is their demand for fish. The use of gillnets (a wall of netting that hangs in the water column) was found to have greatly increased during the two decades that the researchers study took place.

Gillnets catch fish that swim into it and catch them by their gills – S. Maugeri / FAO¹⁰

A recently published study by another group of researchers, Campbell and colleagues¹¹, looked into how fisheries and river dolphins are interacting in the Peruvian Amazon. They used questionnaires that asked about fishing habits, fisher interactions with dolphins, and fisher perceptions and beliefs regarding boto and tucuxi dolphins. Community members who were not directly involved in fishing were also given questionnaires to gather information about beliefs and perceptions about river dolphins and the selling of dolphin body parts.

Most fishers interviewed by the researchers had a negative perception of river dolphins and stated that they had had conflicts with dolphins in their fishing areas. The biggest problems they reported were dolphins getting tangled up in their nets and damaging fishing gear, dolphins stealing fish, and boto dolphins being aggressive towards their boats. These have economic impacts for fishers.

A big problem in dolphin conservation is dolphin by-catch, where fishers are trying to catch specific types of fish but unintentionally also catch dolphins. The study estimated a minimum of 182 dolphins being unintentionally caught per year across the fishers they surveyed. Given this, there may be upwards of 2,000 dolphins being bycaught over the entire area they sampled when you take into account the estimated 9735 fishers working in the area. Even this is a conservative estimate, given that the catching of dolphins is illegal, and so the fishers who filled out the questionnaires likely reported fewer catches than they would have otherwise. Bycaught dolphins may be released alive, dead, or kept and sold as bait or for traditional use. A third of fishers reported knowing someone who used dolphin parts as bait, and 56% of community member reported knowing where dolphin parts were sold. However, only 26% of community members stated that they knew that river dolphins were a legally protected species. River dolphins are primarily used as bait for the rapidly expanding piracatinga (catfish) fishery in South America, despite this practice being illegal.

In 2015, the Brazilian government announced a 5-year prohibition¹² on the sale and trade of piracatinga with the intention of putting an end to dolphin hunting. River dolphin conservation is challenging because these fishers have no economic alternatives and there is limited presence of governmental organizations and strategies to help deal with this¹³. Fishing is practiced by most families living by the river in these areas to meet basic needs and is also one of the leading economic activities in the Amazon. The annual revenue of fishing activities is approximately 80 million USD in the Peruvian Amazon basin¹¹. It is not surprising then, that the fishers in the state of Amazonas immediately pushed for a reduced length of the ban¹⁴.  Additionally, in their paper, da Silva and colleagues saw no improvement in dolphin numbers from 2015 to 2017, and suggested that this ban was widely ignored⁹.

I have come a long way since that first glimpse into conservation science all those years ago in Peru. I know now that when we see these types of debates, we have to remember that conservation is complex, and everyone has different opportunities, perceptions, and priorities. Conservation isn’t just about counting animals from a riverboat. Efforts to safeguard species have to consider the ecological, economic, and social factors surrounding an issue to truly be effective. In this case, clear and enforceable regulations have to be put in place by the government to protect river dolphins. The 5-year ban on piracatinga sale, for example, expired in January 2020 and has not been renewed¹⁵. Research into population trends must continue, as well as ways to decrease bycatch. Finally, increased efforts must be put into decreasing the economic reliance of fishers on the sales of river dolphins for bait in the Amazon basin.

Although the thought of juggling all these components of conservation can seem daunting at times, the challenge and the reward of successful conservation and management are worth the effort. I can only hope that more people will rise to the challenge to help the animal that ignited my passion for wildlife conservation all those years ago.

References

1.        Mr Devotor. The Facts of Amazon River Dolphins. https://www.charismaticplanet.com/facts-amazon-river-dolphins/ (2019).

2.        Mann, G. R. Tucuxi Dolphin. 2019 http://otlibrary.com/tucuxi-dolphin/.

3.        Operation Wallacea. Conservation Research Expeditions. https://www.opwall.com/ (2020).

4.        PROMPERU. Pacaya Samiria Nature Reserve. https://www.peru.travel/en/attractions/pacaya-samiria-national-reserve.

5.        IUCN. International Union for Conservation of Nature . https://www.iucn.org/ (2020).

6.        IUCN Red List. The IUCN Red List of Threatened Species. https://www.iucnredlist.org/ (2020).

7.        Secchi, E. Sotalia fluviatilis. The IUCN Red List of Threatened Species 2012. e.T190871A17583369. https://dx.doi.org/10.2305/IUCN.UK.2012.RLTS.T190871A17583369.en (2020).

8.        da Silva, V. et al. Inia geoffrensis. The IUCN Red List of Threatened Species 2018: e.T10831A50358152. https://dx.doi.org/10.2305/IUCN.UK.2018-2.RLTS.T10831A50358152.en (2018).

9.        Da Silva, V. M. F., Freitas, C. E. C., Dias, R. L. & Martin, A. R. Both cetaceans in the Brazilian Amazon show sustained, profound population declines over two decades. PLoS One 13, e0191304 (2018).

10.      Maugeri, S. fishing with bottom gillnets. FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS FAO http://www.fao.org/3/X6935E/X6935E00.htm (1980).

11.      Campbell, E. et al. Coexisting in the Peruvian Amazon: Interactions between fisheries and river dolphins. J. Nat. Conserv. 56, 125859 (2020).

12.      IUCN – SSC Cetacean Specialist Group. Amazon dolphins as fish bait: Brazil introduces a moratorium on piracatinga fishing. https://iucn-csg.org/amazon-dolphins-as-fish-bait-brazil-introduces-a-moratorium-on-piracatinga-fishing/ (2019).

13.      Trujillo, F., Crespo, E., Van Damme, P. A. & Usma, J. S. The Action Plan for South American River Dolphins 2010-2020. (WWF, Fundación Omacha, WDS, WDCS, Solamac, 2010).

14.      InfoAmazonia. Pescadores do Amazonas querem reduzir tempo da moratória da piracatinga (EN: Fishermen from Amazonas want to reduce the moratorium on piracatinga). 2015 https://infoamazonia.org/pt/2015/03/amazon-fishermen-want-to-reduce-time-of-moratorium-on-piracatinga-fish/#!/story=post-12510&loc=-4.389559200000014,-64.55674760000001,7.

15.      Mongabay - EcoWatch. Brazil’s Amazon River Dolphin Faces Extinction After Fishing Moratorium Ends. https://www.ecowatch.com/amazon-river-dolphin-2646191674.html?rebelltitem=1#rebelltitem1 (2020).

Increasing diversity of COVID-19 strains: insights into evolutionary divergence and public health

 To be clear, I am not a virologist, nor am I a public health expert. But I do know how to analyze patterns of evolutionary diversity. Research into the SARS-CoV-2 virus that has given rise to the COVID-19 pandemic has greatly enhanced our understanding of global disease dynamics, mRNA vaccines and public health responses to a global crisis. But the COVID-19 pandemic also has the potential to provide fundamental insights into basic ecological and evolutionary processes. 

While a lot has been written about how COVID-19 lock-downs have had noticeable repercussions on air quality and wildlife in cities, the virus lends itself as a microcosm into natural world dynamics. SARS-CoV-2 is now the most studied non-human organism on Earth, and we've witnessed its spread across the globe (which provides insights into invasion biology), it has spread exponentially in populations at times (showcasing the power of models to predict spread), and its rapid diversification is evolution in real time.

Understanding how SARS-CoV-2 strain diversity is generated is of fundamental importance for public health policies. And SARS-CoV-2 is evolving and diversifying. In Ontario, Canada, we have a wonderful resource from Public Health Ontario that publishes data on the evolution of strain diversity and provides a wonderful graphical interface. This interface focuses on the SARS-CoV-2 phylogeny (that is the evolutionary family tree connecting strains to their ancestors) in Ontario.

An example phylogeny

Using their open data, I addressed a simple question, is the evolutionary diversity (measured by the distances separating strains) increasing over time?

To test this, I calculated a statistical measure called the standardized effect size of the mean pairwise distances (SES.MPD) which quantifies the average distances separating strains standardized by random permutations (in this case 500 randomizations) so that a SES.MPD value of 0 means that the evolutionary diversity of a group of strains is no different than a same number of strains randomly selected from the phylogeny. Negative values mean that strains are more closely related on the phylogeny than you expect by chance (referred to as under-dispersed), and positive values mean strains are more distantly related (over-dispersed). I did these calculations for each month since the pandemic hit Ontario (March 2020) and for the seven different regions of Ontario.

Analysis of the standardized effect size of the mean pairwise distances (SES.MPD) of SARS-CoV-2 strains across the seven regions in Ontario since the start of the pandemic. The dashed horizontal line indicates a value of 0 (no different than random expectation) and points outside of the grey box are statistically significantly different than random.

What I found was that early on in the pandemic, the strains were under-dispersed, meaning that they were more closely related and genetically similar than expected by chance. But over time the dissimilarity between strains increases and by May 2021 (the last data in the graphs), many of Ontario's regions had significantly over-dispersed strains. This means that strains found in the populations in May 2021 were generally more dissimilar from one another than early on.

Why this matters is that vaccines and other treatments are typically developed on a single strain or from samples collected at a specific time point. If strains are relatively genetically similar, then it is highly probable that treatments will be successful across the strains. However, as strains diversify and become more dissimilar, then treatments might become less effective overall. 

Had the spreading infection been dominated by single strains, with very few newer strains replacing older ones, we would expect that the SES.MPD values remain below zero, and would make it easier to track strains and adapt treatments.

These patterns are also valuable for insights into ecology and evolution. We often look at SES.MPD values to interpret how different processes structure diversity (like competition, predation, pollution, etc.), but we often don't have good evidence of how historical evolutionary processes can drive SES.MPD differences. The plots above show that rapid evolutionary diversification results in linearly increasing SES.MPD values.